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authorAlexander Kabui2022-01-14 03:14:36 +0300
committerBonfaceKilz2022-01-22 09:23:14 +0300
commit0af9e6a90fa2a65bcd2c1c6d9c6e47b9f099ec85 (patch)
tree6e60a4656080c16c61e4de757ffaf63460ea662c /scripts
parent3ab0c245d2bbfe695b5892e5a1a11c78b2cbce50 (diff)
downloadgenenetwork3-0af9e6a90fa2a65bcd2c1c6d9c6e47b9f099ec85.tar.gz
minor refactoring
Diffstat (limited to 'scripts')
-rw-r--r--scripts/ctl_analysis.R35
1 files changed, 17 insertions, 18 deletions
diff --git a/scripts/ctl_analysis.R b/scripts/ctl_analysis.R
index ff7aa94..dd47759 100644
--- a/scripts/ctl_analysis.R
+++ b/scripts/ctl_analysis.R
@@ -59,6 +59,13 @@ genImageRandStr <- function(prefix){
}
+genRandomFileName <- function(prefix,file_ext=".png"){
+
+ randStr = paste(prefix,stri_rand_strings(1, 9, pattern = "[A-Za-z0-9]"),sep="_")
+
+ return(paste(randStr,file_ext,sep=""))
+}
+
# #output matrix significant CTL interactions with 4 columns: trait, marker, trait, lod
ctl_significant <- CTLsignificant(ctls,significance = 0.05)
@@ -69,7 +76,7 @@ colnames(ctl_significant) = c("trait","marker","trait_2","LOD","dcor")
# # Create the lineplot
-imageLoc = file.path(input$imgDir,genImageRandStr("CTLline"))
+imageLoc = file.path(input$imgDir,genRandomFileName("CTLline"))
png(imageLoc,width=1000,height=600,type='cairo-png')
@@ -84,7 +91,7 @@ ctl_plots = c()
for (trait in phenoData$trait_db_list)
{
- image_loc = file.path(input$imgDir,genImageRandStr(paste("CTL",n,sep="")))
+ image_loc = file.path(input$imgDir,genRandomFileName(paste("CTL",n,sep="")))
png(image_loc,width=1000, height=600, type='cairo-png')
plot.CTLobject(ctls,n-1,significance= 0.05, main=paste("Phenotype",trait,sep=""))
@@ -97,18 +104,18 @@ for (trait in phenoData$trait_db_list)
# rename coz of duplicate key names
-network_file_path = file.path(input$imgDir,paste("ctlnet","randomz",sep=""))
-
+# refactor this
-file.create(network_file_path)
+network_file_name = paste("ctlnet",stri_rand_strings(1, 9, pattern = "[A-Za-z0-9]"),sep="_")
+netfile = file.path(input$imgDir,paste(network_file_name,".sif",sep=""))
+nodefile = file.path(input$imgDir,paste(network_file_name,".nodes",sep=""))
+# temp fix override ctlnetwork function to target gn2 use case
+# xtodo refactor function
-# temp fix override ctlnetwork function to target certain output file
-
-
-CTLnetworkGn<- function(CTLobject, mapinfo, significance = 0.05, LODdrop = 2, what = c("names","ids"), short = FALSE, add.qtls = FALSE, file = "",tmpDir = "",verbose = TRUE){
+CTLnetworkGn<- function(CTLobject, mapinfo, significance = 0.05, LODdrop = 2, what = c("names","ids"), short = FALSE, add.qtls = FALSE,verbose = TRUE){
if(missing(CTLobject) || is.null(CTLobject)) stop("argument 'CTLobject' is missing, with no default")
if("CTLscan" %in% class(CTLobject)) CTLobject = list(CTLobject)
if(length(what) > 1) what = what[1]
@@ -117,16 +124,8 @@ CTLnetworkGn<- function(CTLobject, mapinfo, significance = 0.05, LODdrop = 2, wh
significant <- CTLsignificant(CTLobject, significance, what = "ids")
if(!is.null(significant)){
all_m <- NULL; all_p <- NULL;
- nodefile=""; netfile = "";
- if(file != ""){
- netfile = file.path(tmpDir,paste("ctlnet",file,".sif",sep=""))
- nodefile = file.path(tmpDir,paste("ctlnet",file,".nodes",sep=""))
-
- # netfile <- paste("ctlnet",file,".sif",sep="")
- # nodefile <- paste("ctlnet",file,".nodes",sep="")
- }
cat("",file=netfile); cat("",file=nodefile);
if(verbose) cat("NETWORK.SIF\n")
edges <- NULL
@@ -214,7 +213,7 @@ CTLnetwork.addmarker <- function(markers, mapinfo, name, realname){
# generating network
-ctl_network = CTLnetworkGn(ctls, significance = 0.05, LODdrop = 2,short = FALSE, add.qtls = FALSE,tmpDir=input$imgDir,file = "random", verbose = TRUE)
+ctl_network = CTLnetworkGn(ctls, significance = 0.05, LODdrop = 2,short = FALSE, add.qtls = FALSE, verbose = TRUE)